Compositions and methods for treatment of latent viral infections

Abstract

Methods for treating latent viral infections using a gene for a nuclease that is expressed in the presence of a latent viral infection, allowing the nuclease to digest viral nucleic acid. The gene is controlled by a switch that turns expression on in the presence of viral transcripts. The switch may be an engineered sequence that, in the absence of a viral transcript, forms a duplex structure to inhibit translation. The viral transcript hybridizes to the switch and disrupts the duplex structure, allowing translation to occur. A nucleic acid encodes a nuclease and a switch that causes the nuclease to be expressed in the presence of a viral nucleic acid. A portion of the switch may be complementary to at least a portion of a latency associated transcript such as an HHV latency associated transcript that, when present, interacts with the switch to initiate translation of the nuclease.

What is claimed is: 
     
         1 . A nucleic acid that encodes:
 a nuclease; and   a switch that causes the nuclease to be expressed in the presence of a viral nucleic acid.   
     
     
         2 . The nucleic acid of  claim 1 , wherein a portion of the switch is complementary to at least a portion of a latency associated transcript. 
     
     
         3 . The nucleic acid of  claim 2 , wherein the latency associated transcript comprises one selected from the group consisting of: an HHV latency associated transcript; and a latency-associated transcript of pseudorabies virus. 
     
     
         4 . The nucleic acid of  claim 2 , wherein the latency associated transcript when present interacts with the switch to initiate translation of the nuclease. 
     
     
         5 . The nucleic acid of  claim 4 , wherein the nucleic acid is a plasmid. 
     
     
         6 . The nucleic acid of  claim 1 , wherein the nucleic acid is mRNA comprising a 5′ cap and poly(A) tail. 
     
     
         7 . The nucleic acid of  claim 5 , wherein the nuclease is Cas9 endonuclease. 
     
     
         8 . The nucleic acid of  claim 7 , wherein the nucleic acid further encodes a guide sequence that targets the nuclease to a target on a genome of a virus. 
     
     
         9 . The nucleic acid of  claim 8 , wherein the target comprises a segment of at least 18 nucleotides that is at least 60% complementary to the guide sequence and is adjacent a protospacer adjacent motif (PAM), and wherein the target is not found in the host genome. 
     
     
         10 . The nucleic acid of  claim 9 , wherein the target in the viral genome includes a portion of a genome or gene of one selected from the group consisting of: a hepatitis virus; a hepatitis B virus (HBV); an Epstein-Barr virus; a Kaposi's sarcoma-associated herpesvirus (KSHV); a herpes-simplex virus (HSV); a cytomegalovirus (CMV); and a human papilloma virus (HPV). 
     
     
         11 . The nucleic acid of  claim 8 , wherein the switch is a riboswitch. 
     
     
         12 . The nucleic acid of  claim 11 , wherein the riboswitch is a portion of the nucleic acid that, when transcribed into mRNA, forms a double stranded structure that blocks translation in the absence of the viral nucleic acid. 
     
     
         13 . The nucleic acid of  claim 12 , wherein the switch includes one or more of a ribosome binding site and a start codon. 
     
     
         14 . The nucleic acid of  claim 13 , wherein when the plasmid is transcribed into RNA and the latency associated transcript hybridizes to the riboswitch, the Cas9 endonuclease is expressed. 
     
     
         15 . The nucleic acid of  claim 1 , wherein the viral nucleic acid required for expression of the nuclease is a latency-associated transcript. 
     
     
         16 . The nucleic acid of  claim 15 , wherein the nuclease is one selected from the group consisting of a zinc-finger nuclease, a transcription activator-like effector nuclease, and a meganuclease. 
     
     
         17 . The nucleic acid of  claim 1 , wherein the switch causes translation of the nuclease upon hybridization of the viral nucleic acid to the switch. 
     
     
         18 . The nucleic acid of  claim 1 , wherein the viral nucleic acid is from a virus selected from the group consisting of adenovirus, herpes simplex virus, varicella-zoster virus, Epstein-Barr virus, human cytomegalovirus, human herpesvirus type 8, human papillomavirus, BK virus, JC virus, smallpox, hepatitis B virus, human bocavirus, parvovirus, B19, human astrovirus, Norwalk virus, coxsackievirus, hepatitis A virus, poliovirus, rhinovirus, sever acute respiratory syndrome virus, hepatitis C virus, yellow fever virus, dengue virus, west nile virus, rubella virus, hepatitis E virus, human immunodeficiency virus, influenza virus, guanarito virus, junin virus, lassa virus, machupo virus, sabia virus, Crimean-Congo hemorrhagic fever virus, ebola virus, Marburg virus, measles virus, mumps virus, parainfluenza virus, respiratory syncytial virus, human metapnemovirus, Hendra virus, nipah virus, rabies virus, hepatitis D virus, rotavirus, orbivirus, coltivirus, and banna virus.